Adds a module to support gtsummary#973
Merged
llrs-roche merged 32 commits intomainfrom Feb 9, 2026
Merged
Conversation
Contributor
|
Code Coverage SummaryDiff against mainResults for commit: 1e27b38 Minimum allowed coverage is ♻️ This comment has been updated with latest results |
Contributor
Unit Tests Summary 1 files 38 suites 24m 23s ⏱️ For more details on these errors, see this check. Results for commit 6403bc2. ♻️ This comment has been updated with latest results. |
Contributor
Unit Test Performance Difference
Additional test case details
Results for commit 7159e43 ♻️ This comment has been updated with latest results. |
osenan
requested changes
Feb 2, 2026
Contributor
osenan
left a comment
osenan
left a comment
There was a problem hiding this comment.
Hi, very good job!
I have provided small comments on function arguments and assertions. I have reviewed the full ui part and all parts of the server that I was confident. The last elements when we "print" the content of the qenv to subsequent qenv looks slightly unknown to me.
I cannot see the table in the example you provided, is it working for you?
On new iteration I will check the documentation.
Contributor
Author
|
Yes the example works as is for me with the devel version of all packages But I see you want to explore a table which summarizes the same column as you split the table by (so to speak the x and y on the table are the same, so the values are empty). Maybe I should check those arguments and provide an informative error on this case, but I thought that teal would provide the library("gtsummary")
library("dplyr")
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
trial |>
select(age, grade, response) |>
tbl_summary(by = "age", include = "age")
#> 11 missing rows in the "age" column have been removed.
#> Error in `rep_named()`:
#> ! `names` must be `NULL` or a character vector, not an empty integer
#> vector.Created on 2026-02-02 with reprex v2.1.1 Edit: I already put some safeguards to prevent that to happen. |
…dules.general into tm_gtsummary
osenan
approved these changes
Feb 2, 2026
Contributor
osenan
left a comment
osenan
left a comment
There was a problem hiding this comment.
Thanks for the changes. I have now tested the app. All the validate::need calls are appearing. Let's find more bugs with more dry runs or with the unit tests let's check the edge cases.
I found this curiosity of calling a hash function on the report:
ADSL <- teal.data::rADSL
stopifnot(rlang::hash(ADSL) == "843e317c3d4aeb88062cd39a9c62fe8a") # @linksto ADSL
.raw_data <- list2env(list(ADSL = ADSL))
lockEnvironment(.raw_data) # @linksto .raw_data
library(crane)
table <- crane::tbl_roche_summary(data = ADSL, by = "SITEID", include = c("SITEID", "ACTARM"), nonmissing = "ifany", percent = "column")
table
Just decide if you want to move the include before the ... or you prefer to keep it where it is. In that case, let's see if it can be set to NULL
6 tasks
Contributor
Author
|
Waiting to merge to see if we can merge a feature complete module with the work on: |
m7pr
reviewed
Feb 4, 2026
m7pr
reviewed
Feb 4, 2026
Contributor
m7pr
left a comment
m7pr
left a comment
There was a problem hiding this comment.
For now reviewed documentation and DESCRIPTION
Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> Signed-off-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
m7pr
reviewed
Feb 4, 2026
m7pr
reviewed
Feb 4, 2026
Contributor
|
So far I was able to run the example from the opening of this PR on a 
Will now try to test with a decorator |
Contributor
|
Also works with a decorator Code# Example: tm_gtsummary with decorators
# This example demonstrates how to use decorators with the tm_gtsummary module.
library(teal.modules.general)
# Setup data
data <- within(teal.data::teal_data(), {
ADSL <- teal.data::rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
# ============================================================================
# Decorator 1: Modifies the gtsummary table header (keeps as gtsummary)
# ============================================================================
# This decorator modifies the table caption using gtsummary functions,
# keeping the table as a gtsummary object (no conversion to gt needed).
table_caption_decorator <- function(default_caption = "Summary Table") {
teal::teal_transform_module(
label = "Table Caption",
ui = function(id) {
ns <- shiny::NS(id)
shiny::tagList(
shiny::textInput(
ns("caption"),
"Table Caption",
value = default_caption
)
)
},
server = function(id, data) {
shiny::moduleServer(id, function(input, output, session) {
shiny::reactive({
req(data())
within(
data(),
{
# Keep the table as gtsummary object
# Modify using gtsummary functions - no conversion to gt needed
if (inherits(table, "gtsummary")) {
# Modify the table caption using gtsummary::modify_caption()
if (nchar(caption) > 0) {
table <- table |>
gtsummary::modify_caption(caption)
}
}
# If it's already gt, leave it as is (shouldn't happen with this decorator)
},
caption = input$caption
)
})
})
}
)
}
# ============================================================================
# Decorator 2: Modifies the gtsummary table output (converts to gt for footnotes)
# ============================================================================
# A decorator modifies the module's output after it's generated.
# This example creates a decorator that adds a footnote and modifies table formatting.
# Note: This one converts to gt because gtsummary doesn't have direct footnote functions.
table_footnote_decorator <- function(default_footnote = "Summary statistics") {
teal::teal_transform_module(
label = "Table Footnote",
ui = function(id) {
ns <- shiny::NS(id)
shiny::tagList(
shiny::textInput(
ns("footnote"),
"Table Footnote",
value = default_footnote
)
)
},
server = function(id, data) {
shiny::moduleServer(id, function(input, output, session) {
shiny::reactive({
req(data())
within(
data(),
{
# The table is a gtsummary object (from crane::tbl_roche_summary)
# We need to convert to gt to add footnotes because gtsummary doesn't have
# a direct tab_footnote() function. The module will handle the gt object
# correctly when displaying.
# Only process if it's still a gtsummary object (not already converted)
if (inherits(table, "gtsummary")) {
# Convert to gt to add footnote
table_gt <- gtsummary::as_gt(table)
if (nchar(footnote) > 0) {
table_gt <- table_gt |>
gt::tab_footnote(
footnote = footnote,
locations = gt::cells_title()
)
}
# Store as gt - the module's table_r reactive handles both gtsummary and gt
table <- table_gt
} else if (inherits(table, "gt_tbl")) {
# Already converted to gt - don't modify again to avoid duplicate footnotes
table <- table
}
},
footnote = input$footnote
)
})
})
}
)
}
# ============================================================================
# Create the app with decorator
# ============================================================================
app <- init(
data = data,
modules = modules(
tm_gtsummary(
by = teal.transform::data_extract_spec(
dataname = "ADSL",
select = teal.transform::select_spec(
choices = c("SEX", "COUNTRY", "SITEID", "ACTARM"),
selected = "SEX",
multiple = FALSE
)
),
include = teal.transform::data_extract_spec(
dataname = "ADSL",
select = teal.transform::select_spec(
choices = c("SITEID", "COUNTRY", "ACTARM"),
selected = "SITEID",
multiple = TRUE,
fixed = FALSE
)
),
# Decorator: Applied to the table output
# This example uses the caption decorator which keeps the table as gtsummary
decorators = list(
table = table_caption_decorator("Demographic Summary Table CAPTION EXTRA")
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
|
# Pull Request Adds tests for #973 TODO: - [x] Test input - [x] Test UI - [x] Test output On a different PR: - [ ] Test decorators: - [ ] One - [ ] Multiple --------- Signed-off-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com> Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com>
Contributor
|
Hey I can confirm I reviewed docs, imports and implementation. 
TODO
|
…dules.general into tm_gtsummary
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes https://github.com/insightsengineering/coredev-tasks/issues/714
Related to https://github.com/insightsengineering/coredev-tasks/issues/676
Adds 3 more package dependencies: (methods), crane, gtsummary, gt. I haven't added minimal version for them.
We could remove crane dependency at the cost of having less corporate style tables (instead of using
crane::tbl_roche_summary()we could have the vanillagtsummary::tbl_summary().Documentation is mostly imported from other packages.
It involves just 3 functions: the module (is this a good name for such module?), the ui and the server function.
Support to download the table depends on insightsengineering/teal.widgets#335.
Test will come once this branch is reviewed, but known corner case from the module: No
includevariables should select all variables except the one used to split the columnsby.Further modifications of the table should be done via decorators not included on this PR.
Adding decorators might involve modifying
check_decorators()to handle more than one decorator for the same object. This function is duplicated on TMG and TMC and I haven't included on the PR but here is the one I was using:Modified check_decorators to work with multiple decorators for the same object
Example: